Jay's lips curled upwards into a snarl. All this sentimental stuff really wasn't in his expertise. Emotions besides anger and hatred were all quite foreign to him. At that moment, he was experiencing both of them. All he really wanted to do was to make the doctor pay for the life he was brought into. 

Simply killing the doctor with a few shots to some major organs was what he had intended..but with the involvement of his son, things just got a whole lot more complicated...and dramatic. He could just pull the trigger, blow his son's brains out, and let the doctor live on. He would grieve and mourn, sure, but something told Jay the doctor was capable of moving past his son's death. In the end, it would just make him even angrier that Jay was, and possibly make him thirsty for revenge. He couldn't give me some anticlimactic ending in with they both died in each other's arms either. Especially when it's what they wanted..neither would be alone and both would be free from the government. 

Jay went through the scenarios in his head, and almost smiled when he picked what he thought was the best one. The one where the doctor suffered through something greater than simply his son's death. 

Jay pressed the gun harder into Leonel's skull and leaned his face closer to the Doctor. "Leave," he snarled, "Go back to your living quarters at the facility or hide, I don't care which. Your son stays with me." Jay paused when he saw the Doctor open and close his mouth like a fish, no words coming out to express his horror. "And don't even think about sending some big bad agent to get me. I've been around for plenty of years nod trust me. I. Know. All. Of. Them." He said, the last few words dripping with venom as he put on his most menacing smirk. "Now leave."